{"action":"created","issue":{"url":"https://api.github.com/repos/joey711/phyloseq/issues/816","repository_url":"https://api.github.com/repos/joey711/phyloseq","labels_url":"https://api.github.com/repos/joey711/phyloseq/issues/816/labels{/name}","comments_url":"https://api.github.com/repos/joey711/phyloseq/issues/816/comments","events_url":"https://api.github.com/repos/joey711/phyloseq/issues/816/events","html_url":"https://github.com/joey711/phyloseq/issues/816","id":255678329,"number":816,"title":"Obtaining and/or plotting ordination scores other than \"scaling 2\"/correlation biplots","user":{"login":"JacobRPrice","id":11934394,"avatar_url":"https://avatars3.githubusercontent.com/u/11934394?v=4","gravatar_id":"","url":"https://api.github.com/users/JacobRPrice","html_url":"https://github.com/JacobRPrice","followers_url":"https://api.github.com/users/JacobRPrice/followers","following_url":"https://api.github.com/users/JacobRPrice/following{/other_user}","gists_url":"https://api.github.com/users/JacobRPrice/gists{/gist_id}","starred_url":"https://api.github.com/users/JacobRPrice/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JacobRPrice/subscriptions","organizations_url":"https://api.github.com/users/JacobRPrice/orgs","repos_url":"https://api.github.com/users/JacobRPrice/repos","events_url":"https://api.github.com/users/JacobRPrice/events{/privacy}","received_events_url":"https://api.github.com/users/JacobRPrice/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2017-09-06T17:11:27Z","updated_at":"2017-09-06T18:35:18Z","closed_at":null,"author_association":"NONE","body":"Hi Everyone, \r\n\r\nLooking through the documentation and functions for ordinate() and plot_ordination() and I've noticed that there is no option to designate what \"scaling\" of scores is returned by those functions. My understanding is that the default behavior of vegan is to return \"scaling type 2\" scores when prompted, and that this type of scaling is typically used to interrogate the relationships between species while approximating distances/structures amongst sites/samples. \r\n\r\n1. Did I miss something in the documentation that allows an argument along the lines of \"scaling=2\" (as in plot.cca() within vegan)? I was thinking it could be automatically selected based upon the \"type\" argument in plot_ordination() but was unable to locate that functionality.    \r\n2. If not, is there rationale that I'm unaware of for this omission (which could be entirely possible)?  \r\n\r\nThank you for any insight you guys would be able to provide. \r\n\r\nJake"},"comment":{"url":"https://api.github.com/repos/joey711/phyloseq/issues/comments/327574938","html_url":"https://github.com/joey711/phyloseq/issues/816#issuecomment-327574938","issue_url":"https://api.github.com/repos/joey711/phyloseq/issues/816","id":327574938,"user":{"login":"joey711","id":841437,"avatar_url":"https://avatars0.githubusercontent.com/u/841437?v=4","gravatar_id":"","url":"https://api.github.com/users/joey711","html_url":"https://github.com/joey711","followers_url":"https://api.github.com/users/joey711/followers","following_url":"https://api.github.com/users/joey711/following{/other_user}","gists_url":"https://api.github.com/users/joey711/gists{/gist_id}","starred_url":"https://api.github.com/users/joey711/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/joey711/subscriptions","organizations_url":"https://api.github.com/users/joey711/orgs","repos_url":"https://api.github.com/users/joey711/repos","events_url":"https://api.github.com/users/joey711/events{/privacy}","received_events_url":"https://api.github.com/users/joey711/received_events","type":"User","site_admin":false},"created_at":"2017-09-06T18:35:18Z","updated_at":"2017-09-06T18:35:18Z","author_association":"OWNER","body":"@JacobRPrice I don't think there's anything to over-write. Any additional coordinate features in the ordination can be extracted, and added as additional layers to the ggplot object produced by `plot_ordination`.\r\n\r\nMichelle Berry has posted a nice example of this general approach (but for CAP):\r\n\r\nhttp://deneflab.github.io/MicrobeMiseq/demos/mothur_2_phyloseq.html#constrained_ordinations\r\n\r\n"}}
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